How To Dynamically Access Data From Ncbi Database Using Biojava?
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8.1 years ago

How to dynamically access data from NCBI database using biojava?

bioinformatics • 1.9k views
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why do you need BioJava ? A simple call with java.net.URL is enough.

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8.1 years ago
Pavel Senin ★ 1.9k

I am sure new Biojava (3.0+) implements some methods, but I had a good experience fetching sequences with 1.8.2 version using RichSequenceDB class http://www.biojava.org/docs/api1.8.2/org/biojavax/bio/db/ncbi/GenbankRichSequenceDB.html. You'll need to instantiate the class and use the getRichSequence("accession") method. Also, NCBI provides an advanced toolkit for Java using Axis2: http://www.ncbi.nlm.nih.gov/books/NBK55696/.

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8.1 years ago
jlshi.nudt ▴ 220

I always use R package named as GEOquery to get data from NCBI.

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